forester/ruby/evoruby/exe/run_phylo_pipeline.rb

   1 #!/usr/local/bin/ruby -w
   2 #
   3 # = run_phylo_pipeline
   4 #
   5 # Copyright::  Copyright (C) 2010 Christian M. Zmasek
   6 # License::    GNU Lesser General Public License (LGPL)
   7 #
   8 # $Id Exp $
   9 #
  10 #
  11
  12
  13 module Evoruby
  14
  15   class RunPhyloPipeline
  16
  17     PFAM      = "/home/czmasek/DATA/PFAM/PFAM260X/"
  18
  19
  20
  21     def run
  22       unless ARGV.length == 4
  23         error "arguments are: <fasta formatted inputfile> <hmm-name> <min-length> <neg e-value exponent>"
  24       end
  25
  26       hmmscan   = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0/src/hmmscan"
  27       hmmsearch = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0/src/hmmsearch"
  28       hsp       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/hsp.rb"
  29       d2f       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/d2f.rb"
  30       dsx       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/dsx.rb"
  31
  32       base_name   = ARGV[ 0 ]
  33       hmm         = ARGV[ 1 ]
  34       length      = ARGV[ 2 ]
  35       e_value_exp = ARGV[ 3 ]
  36       do_domain_combination_analysis = true
  37
  38       if e_value_exp < 0
  39         error "e-value exponent cannot be negative"
  40       end
  41       if length <= 1
  42         error "length exponent cannot be smaller than or equal to 1"
  43       end
  44
  45       if base_name.downcase.end_with?( ".fasta" )
  46         base_name = base_name[ 0 .. base_name.length - 7 ]
  47       elsif base_name.downcase.end_with?( ".fsa" )
  48         base_name = base_name[ 0 .. base_name.length - 5 ]
  49       end
  50
  51       if do_domain_combination_analysis
  52
  53         puts "hmmscan:"
  54         cmd = "#{hmmscan} --nobias --domtblout #{base_name}_hmmscan_10 -E 10 #{PFAM}Pfam-A.hmm #{base_name}.fasta"
  55         run_command( cmd )
  56         puts
  57
  58         puts "hmmscan to simple domain table:"
  59         cmd = "#{hsp} #{base_name}_hmmscan_10 #{base_name}_hmmscan_10_domain_table"
  60         run_command( cmd )
  61         puts
  62
  63         puts "domain table to forester format:"
  64         cmd = "#{d2f} -e=10 #{base_name}_hmmscan_10_domain_table #{base_name}.fasta #{base_name}_hmmscan_10.dff"
  65         run_command( cmd )
  66         puts
  67
  68       end
  69
  70       puts "hmmsearch:"
  71       cmd = "#{hmmsearch} --nobias -E 1000 --domtblout #{base_name}.hmmsearch_#{hmm}  #{PFAM}PFAM_A_HMMs/#{hmm}.hmm #{base_name}.fasta"
  72       run_command( cmd )
  73       puts
  74
  75       puts "dsx:"
  76       cmd = "#{dsx} -d -e=1e-#{e_value_exp.to_s} -l=#{length} #{hmm} #{base_name}.hmmsearch_#{hmm} #{base_name}.fasta #{base_name}_#{hmm}_e#{e_value_exp.to_s}_#{length}"
  77       run_command( cmd )
  78       puts
  79
  80     end
  81
  82     def run_command( cmd )
  83       puts cmd
  84       `#{cmd}`
  85     end
  86
  87     def error msg
  88       puts
  89       puts msg
  90       puts
  91       exit
  92     end
  93
  94   end
  95
  96   p = RunPhyloPipeline.new()
  97
  98   p.run()
  99
 100 end
 101
 102
 103